Contacts of the strand formed by residues 387 - 393 (chain A) in PDB entry 3UAJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 387 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A LYS* 4.4 14.1 - - - +
306A PHE 3.5 25.0 + - - +
307A SER* 4.6 4.3 - - - -
308A ILE* 3.8 44.0 - - + +
324A VAL* 5.3 2.2 - - + -
378A ILE 3.4 3.5 - - - +
379A VAL* 3.5 2.4 - - - -
380A ILE* 2.8 51.8 + - + +
385A SER 3.8 1.2 + - - -
386A ALA* 1.3 70.7 - - - +
388A THR* 1.3 63.7 + - - +
389A LEU* 3.9 15.9 - - + -
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Residues in contact with THR 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A LYS* 4.7 20.4 + - + +
377A TYR* 3.7 31.9 - - + -
378A ILE 3.4 7.0 - - - +
379A VAL* 4.5 16.0 - - + +
386A ALA* 3.8 8.2 + - - +
387A LEU* 1.3 77.5 + - - +
389A LEU* 1.3 66.2 + - - +
390A HIS 4.5 0.2 + - - -
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Residues in contact with LEU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ILE* 3.9 26.9 - - + -
311A GLU* 5.8 4.3 - - + -
312A MET* 4.9 21.5 - - + +
322A VAL* 5.1 4.9 - - + -
377A TYR* 3.5 6.9 - - - -
378A ILE* 2.8 50.1 + - + +
380A ILE* 3.8 27.4 - - + -
387A LEU* 3.9 22.9 - - + -
388A THR* 1.3 76.3 - - - +
390A HIS* 1.3 65.0 + - - +
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Residues in contact with HIS 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A MET* 5.1 0.2 - - - +
342A VAL* 5.9 0.9 - - + -
375A ASP* 3.2 37.8 + - + -
376A SER 3.8 2.4 + - - -
377A TYR* 3.3 44.2 + + + -
388A THR 4.5 0.2 + - - -
389A LEU* 1.3 76.3 - - - +
391A TRP* 1.3 80.0 + - - +
392A PHE* 4.9 4.7 - - + +
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Residues in contact with TRP 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A GLU* 5.2 4.7 - - - -
312A MET* 3.5 56.3 - - + -
313A ALA* 4.4 1.3 - - - -
314A GLU* 3.6 44.4 + - + -
320A THR* 3.5 16.8 - - + +
371A PRO* 3.7 25.4 - - + +
374A GLY 3.4 0.5 - - - +
375A ASP* 3.5 2.3 - - - -
376A SER* 2.9 45.5 + - - +
378A ILE* 4.7 4.7 - - + -
390A HIS* 1.3 86.0 - - - +
392A PHE* 1.3 87.7 + - - +
393A ARG* 4.3 2.6 - - + +
107B LEU* 6.1 2.7 - - + -
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Residues in contact with PHE 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A GLU* 4.6 1.6 - - - +
374A GLY* 3.4 26.0 - - - -
375A ASP* 3.5 29.6 - - - +
390A HIS* 4.9 4.9 - - + +
391A TRP* 1.3 92.2 + - - +
393A ARG* 1.3 65.4 + - - +
394A LYS* 4.2 29.3 + - + +
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Residues in contact with ARG 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A GLU* 3.5 19.5 - - - +
317A HIS 3.8 19.4 + - - -
318A GLY* 3.9 24.6 + - - -
319A THR* 6.2 0.2 - - - +
370A GLU* 4.2 19.8 + - - +
371A PRO* 2.9 29.0 + - - +
372A PRO* 3.5 21.1 - - - +
373A PHE* 3.7 40.3 - - + +
374A GLY* 3.0 28.2 + - - -
391A TRP* 4.3 7.8 - - + +
392A PHE* 1.3 77.5 - - - +
394A LYS* 1.3 69.3 + - - +
395A GLY 3.9 0.7 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il